Software Open Access

Model source code to "Plague and human ectoparasites: a new model for an old disease"

Dean, Katharine R.; Stenseth, Nils Chr.; Krauer, Fabienne; Walløe, Lars; Lingjærde, Ole Christian; Bramanti, Barbara; Schmid, Boris V.

Plague, caused by the bacterium Yersinia pestis, can spread through human populations by multiple transmission pathways. Today, most human plague cases are bubonic, caused by spillover of infected fleas from rodent epizootics, or pneumonic, caused by inhalation of infectious droplets. However, little is known about the historical spread of plague in Europe during the Second Pandemic (14-19th centuries), including the Black Death, which led to high mortality and recurrent epidemics for hundreds of years. Several studies have suggested that human ectoparasite vectors, such as human fleas (Pulex irritans) or body lice (Pediculus humanus humanus), caused the rapidly spreading epidemics. Here we describe a novel compartmental model for plague transmission by a human ectoparasite vector. Using Bayesian inference, we found that this model fits mortality curves from nine outbreaks in Europe better than models for pneumonic or rodent transmission. Our results support that human ectoparasites were primary vectors for plague during the Second Pandemic, including the Black Death (1346-1353), ultimately challenging the assumption that plague in Europe was predominantly spread by rats.

The files in this repository contain the source code for the three transmission models tested in the publication, for one of the nine cities.

Files (24.0 kB)
Name Size
pymc2_human_ectoparasite_barcelona.ipynb
md5:0c2c980f6b1648b896bd9b2f7e44244a
8.2 kB Download
pymc2_pneumonic_barcelona.ipynb
md5:bdbd16f3761a1906010b7408499b7aa7
6.1 kB Download
pymc2_rats_barcelona.ipynb
md5:5635681764b004c67b8e2299936605cf
9.7 kB Download
131
25
views
downloads
All versions This version
Views 131131
Downloads 2525
Data volume 203.3 kB203.3 kB
Unique views 125125
Unique downloads 1313

Share

Cite as